Using various existing protein structure prediction tools, we have built a plausible model of the 327-residue mesothelin molecule. (Sathyanarayana et al, manuscript in review). In the mean time, Dr. Mitchell Ho of the Antibody Therapy Unit (Laboratory of Molecular Biology) determined that only the N-terminal 64-residue portion of mesothelin binds MUC16. Predicting the structure of a 64-residue protein is more difficult than that of a 327-residue chain because small molecule structures must be determined by an ab initio technique, whereas the structure of a larger molecule can often be obtained by recognizing homology to an existing structure (fold recognition). We obtained several possible structures for the 64-residue unit using existing structure prediction servers, which are related, but not the same as that found in the model of the full 327-residue mesothelin molecule. We will select the most plausible one from these models by searching through sugar-binding protein structures for a protein that has a similar structure as that of the model. We are currently collecting and examining the structures of carbohydrate-protein complexes. Also, a protein with 64 residues can be simulated using straight "Molecular Dynamics" technique. We will do such simulation calculations on different models and see which, if any, structure is stable. The stable structure is more likely to be the correct structure. If we obtain a carbohydrate-protein complex structure from the database in which the protein portion is similar to one of the model structures, we already have a good trial mesothelin-carbohydrate complex structure. Otherwise, we will use existing programs to predict carbohydrate binding sites and build a model of the complex. Such a model will not be highly accurate, particularly because we do not know the structure of the MUC16 carbohydrate that binds mesothelin. But we hope that the model will be good enough to suggest the residues that interact with the carbohydrate. Dr. Ho can verify these residues by measuring the changes in binding to MUC16 upon mutating them. We will refine our model by incorporating these experimental data. Once we have such a model, we can start designing the inhibitor molecules.